User blog comment:KanameTousen/Nelo Angelo/@comment-775152-20120403180710

It is implied that Dante killed Vergil. If we remember way back to when DMC1 first came out, it was not intended to be a whole series, so there wasn't any need to keep Vergil around. However; there have since been several instances of killed/defeated bosses coming back in one form or another, such as Echidna and Berial returning to "life" inside The Savior. Additionally, Dante tells Mundus himself to "give my regards to my son," or something to that effect, after he defeats Mundus. This suggests that, though Mundus has been killed, there's some way for him to return.

We can also examine the game world itself for some possible explanations to the question of "Where did Vergil go?" For instance, The Demon World is hinted at being the afterlife for evil humans, just like our notion of Hell. So if you kill an evil person, like Vergil arguably is, would his soul then go to the demon world? If Vergil redeemed himself, might he go to "heaven" and sill be alive there? If Demons are fallen Angels, then there's still the possibility that Vergil, as an Angel, could be "alive" and come back to The Human World.

To summarize my theory, Vergil is in a state akin to that of Schrodinger's cat: he's in a situation where he should be dead, but we can't know for certain and probably won't know unless he comes walzing out of his box.